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2. Method
2.1 Equations of motion
Classical molecular dynamics (MD) is based on Newtonian mechanics: the properties of a set of atoms or particles are determined by studying the trajectory of each particle over time. To do this, the laws of classical mechanics are applied to atoms, which are assimilated to a point mass. For all atoms i in a system, the classical equations of motion are solved simultaneously:
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Method
Examples of molecular dynamics applications
Bibliography
Software tools
Given the power of computational tools and the simplicity of (often open-source) molecular dynamics software, it's relatively easy for any engineer or researcher with a little time on their hands to "get started": documentation is often very well written and includes tutorials or examples that are relatively easy to implement. Below is a list of the main distributions available. However, it is far more effective to start...
Molecular Dynamics Distributions
AMBER (Assisted Model Building and Energy Refinement) http://ambermd.org/ Univ. California. Version 10 (April 2008). Paying under license (Rech./Educ. $400 – Enterprise: $25,000). Dedicated to organic molecules.
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